Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells

J Microbiol Methods. 2006 Nov;67(2):310-20. doi: 10.1016/j.mimet.2006.04.015. Epub 2006 Jun 5.


The differentiation between live and dead bacterial cells presents an important challenge in many microbiological applications. Due to the persistence of DNA in the environment after cells have lost viability, DNA-based detection methods cannot differentiate whether positive signals originate from live or dead bacterial targets. We present here a novel chemical, propidium monoazide (PMA), that (like propidium iodide) is highly selective in penetrating only into 'dead' bacterial cells with compromised membrane integrity but not into live cells with intact cell membranes/cell walls. Upon intercalation in the DNA of dead cells, the photo-inducible azide group allows PMA to be covalently cross-linked by exposure to bright light. This process renders the DNA insoluble and results in its loss during subsequent genomic DNA extraction. Subjecting a bacterial population comprised of both live and dead cells to PMA treatment thus results in selective removal of DNA from dead cells. We provide evidence that this chemical can be applied to a wide range of species across the bacterial kingdom presenting a major advantage over ethidium monoazide (EMA). The general application of EMA is hampered by the fact that the chemical can also penetrate live cells of some bacterial species. Transport pumps actively export EMA out of metabolically active cells, but the remaining EMA level can lead to substantial loss of DNA. The higher charge of PMA might be the reason for the higher impermeability through intact cell membranes, thus avoiding DNA loss.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Azides / chemistry*
  • Cell Survival / physiology*
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • DNA, Bacterial / isolation & purification*
  • Gram-Negative Bacteria / genetics
  • Gram-Negative Bacteria / growth & development*
  • Gram-Positive Bacteria / genetics
  • Gram-Positive Bacteria / growth & development*
  • Intercalating Agents / chemistry*
  • Light
  • Microscopy, Fluorescence
  • Polymerase Chain Reaction
  • Propidium / analogs & derivatives*
  • Propidium / chemistry*


  • Azides
  • DNA, Bacterial
  • Intercalating Agents
  • propidium monoazide
  • Propidium
  • 8-azidoethidium